diff --git a/etc/versions b/etc/versions
index 69ce6d01d4b812e7c13c3635e7140f30aafd7d10..b105c977f79bcb81a3fab613b1cc642626074781 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 15.0.9
-ACT Release 12.0.9
+Artemis Release 15.0.10
+ACT Release 12.0.10
DNAPlotter Release 1.11
BamView 1.2.9
diff --git a/uk/ac/sanger/artemis/components/FeatureEdit.java b/uk/ac/sanger/artemis/components/FeatureEdit.java
index b62005fdedbefc29ce8940fda7bd37f58cdfb1e1..9fb8152762790418ca66a6651fe0d3d2d877f85f 100644
--- a/uk/ac/sanger/artemis/components/FeatureEdit.java
+++ b/uk/ac/sanger/artemis/components/FeatureEdit.java
@@ -50,6 +50,7 @@ import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.StreamQualifier;
import uk.ac.sanger.artemis.io.QualifierInfo;
+import uk.ac.sanger.artemis.io.ValidateFeature;
import uk.ac.sanger.artemis.components.ProgressThread;
import uk.ac.sanger.artemis.components.genebuilder.BasicGeneBuilderFrame;
@@ -606,135 +607,6 @@ public class FeatureEdit extends JPanel
}
});
- /*if(Options.getOptions().getProperty("external_editor") != null)
- {
- final JButton external_fasta_edit_button = new JButton("MESS/FASTA");
- location_button_panel.add(external_fasta_edit_button);
- external_fasta_edit_button.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- if(getFeature().getQualifierByName("fasta_file") != null)
- {
- final String DEFAULT_MAX_EUK_FASTA_HITS = "10";
- final String max_fasta_hits;
-
- final String max_fasta_hits_from_options =
- Options.getOptions().getProperty("mess_fasta_hits");
-
- if(Options.getOptions().isEukaryoticMode())
- {
- if (max_fasta_hits_from_options == null)
- max_fasta_hits = DEFAULT_MAX_EUK_FASTA_HITS;
- else
- max_fasta_hits = max_fasta_hits_from_options;
-
- externalEdit(new String[] { "-fasta", "-maxhits",
- max_fasta_hits, "-euk" });
- }
- else
- {
- if(max_fasta_hits_from_options == null)
- {
- externalEdit(new String[] { "-fasta" });
- }
- else
- {
- externalEdit(new String[] { "-fasta", "-maxhits",
- max_fasta_hits_from_options });
- }
- }
- return;
- }
- } catch(InvalidRelationException _) {}
-
- new MessageDialog(frame,
- "nothing to edit - no /fasta_file qualifier");
- }
- });
-
- final JButton external_blastp_edit_button = new JButton("MESS/BLASTP");
- location_button_panel.add(external_blastp_edit_button);
- external_blastp_edit_button.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- if(getFeature().getQualifierByName("blastp_file") != null)
- {
- final String DEFAULT_MAX_BLASTP_HITS = "10";
- final String max_blastp_hits;
-
- final String max_blastp_hits_from_options =
- Options.getOptions().getProperty("mess_blastp_hits");
-
- if(max_blastp_hits_from_options == null)
- max_blastp_hits = DEFAULT_MAX_BLASTP_HITS;
- else
- max_blastp_hits = max_blastp_hits_from_options;
-
- if(Options.getOptions().isEukaryoticMode())
- {
- externalEdit(new String[] { "-blastp", "-maxhits",
- max_blastp_hits, "-euk" });
- }
- else
- {
- externalEdit(new String[] { "-blastp", "-maxhits",
- max_blastp_hits });
- }
- return;
- }
- } catch(InvalidRelationException _) {}
-
- new MessageDialog(frame,
- "nothing to edit - no /blastp_file qualifier");
- }
- });
-
- final JButton external_go_edit_button = new JButton("MESS/GO");
- location_button_panel.add(external_go_edit_button);
- external_go_edit_button.addActionListener(new ActionListener ()
- {
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- if(getFeature().getQualifierByName("blastp+go_file") != null)
- {
- final String DEFAULT_MAX_GO_BLAST_HITS = "10";
- final String max_go_blast_hits;
-
- final String max_go_blast_hits_from_options =
- Options.getOptions ().getProperty ("mess_blast_go_hits");
-
- if (max_go_blast_hits_from_options == null)
- max_go_blast_hits = DEFAULT_MAX_GO_BLAST_HITS;
- else
- max_go_blast_hits = max_go_blast_hits_from_options;
-
- if(Options.getOptions().isEukaryoticMode())
- {
- externalEdit(new String[] { "-blastp+go", "-maxhits",
- max_go_blast_hits, "-euk" });
- }
- else
- {
- externalEdit(new String[] { "-blastp+go", "-maxhits",
- max_go_blast_hits });
- }
- return;
- }
- } catch(InvalidRelationException _) {}
-
- new MessageDialog(frame,
- "nothing to edit - no /blastp+go_file qualifier");
- }
- });
- }*/
if(Options.isUnixHost())
{
@@ -759,7 +631,7 @@ public class FeatureEdit extends JPanel
StringReader strRead = new StringReader(qualifier_txt);
BufferedReader buff = new BufferedReader(strRead);
String line;
- final Hashtable dataFile = new Hashtable();
+ final Hashtable<String, Vector<String>> dataFile = new Hashtable<String, Vector<String>>();
try
{
int ind;
@@ -776,11 +648,11 @@ public class FeatureEdit extends JPanel
if(ind > -1)
line = line.substring(0, ind);
- Vector v;
+ Vector<String> v;
if(dataFile.containsKey("fasta"))
- v = (Vector)dataFile.get("fasta");
+ v = dataFile.get("fasta");
else
- v = new Vector();
+ v = new Vector<String>();
v.add(line);
dataFile.put("fasta",v);
}
@@ -795,11 +667,11 @@ public class FeatureEdit extends JPanel
if(ind > -1)
line = line.substring(0, ind);
- Vector v;
+ Vector<String> v;
if(dataFile.containsKey("blastp"))
- v = (Vector)dataFile.get("blastp");
+ v = dataFile.get("blastp");
else
- v = new Vector();
+ v = new Vector<String>();
v.add(line);
dataFile.put("blastp",v);
}
@@ -813,11 +685,11 @@ public class FeatureEdit extends JPanel
if(ind > -1)
line = line.substring(0, ind);
- Vector v;
+ Vector<String> v;
if(dataFile.containsKey("blastp+go"))
- v = (Vector)dataFile.get("blastp+go");
+ v = dataFile.get("blastp+go");
else
- v = new Vector();
+ v = new Vector<String>();
v.add(line);
dataFile.put("blastp+go",v);
}
@@ -1028,9 +900,9 @@ public class FeatureEdit extends JPanel
final DatabaseDocument originalDocument =
(DatabaseDocument)((DocumentEntry)edit_feature.getEmblFeature().getEntry()).getDocument();
- final Set uniquenames = ((GFFStreamFeature)edit_feature.getEmblFeature()).getSegmentRangeStore().keySet();
- final Iterator it = uniquenames.iterator();
- final String uniquename = (String)it.next();
+ final Set<String> uniquenames = ((GFFStreamFeature)edit_feature.getEmblFeature()).getSegmentRangeStore().keySet();
+ final Iterator<String> it = uniquenames.iterator();
+ final String uniquename = it.next();
final DatabaseDocument newDocument = new DatabaseDocument(originalDocument,
uniquename, null, true, null);
newDocument.setLazyFeatureLoad(false);
@@ -1287,7 +1159,7 @@ public class FeatureEdit extends JPanel
StringReader strRead = new StringReader(qualifier_txt);
BufferedReader buff = new BufferedReader(strRead);
String line;
- final Vector qual_str = new Vector();
+ final Vector<String> qual_str = new Vector<String>();
try
{
while((line = buff.readLine()) != null)
@@ -1295,26 +1167,23 @@ public class FeatureEdit extends JPanel
}
catch(IOException ioe){}
- Comparator comparator = new Comparator()
+ Comparator<String> comparator = new Comparator<String>()
{
- public int compare (Object fst, Object snd)
+ public int compare (String fst, String snd)
{
- if( !((String)fst).startsWith("/GO") ||
- !((String)snd).startsWith("/GO") )
+ if( !fst.startsWith("/GO") ||
+ !snd.startsWith("/GO") )
return 0;
-
- return ((String)fst).compareTo((String)snd);
+ return fst.compareTo(snd);
}
};
-
Collections.sort(qual_str, comparator);
StringBuffer buffer = new StringBuffer();
for(int i = 0; i < qual_str.size(); i++)
{
final String qualifier_string =
- (String)qual_str.elementAt(i);
-
+ qual_str.elementAt(i);
buffer.append(tidyHelper(qualifier_string) + "\n");
}
@@ -1845,6 +1714,17 @@ public class FeatureEdit extends JPanel
qualifiers.addAll(orthologQualifiers);
}
+ final String goErrs = ValidateFeature.validateGO(qualifiers, getEntryInformation());
+ if(goErrs.length()>0)
+ {
+ Object[] options = { "CANCEL", "CONTINUE" };
+ int opt = JOptionPane.showOptionDialog(null, goErrs, "GO errors",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+
+ if(opt == 0)
+ return false;
+ }
//if(similarityTextArea != null)
// similarityTextArea.checkForChanges();
}